ibllib.oneibl.registration

Functions

get_local_data_repository	Get local data repo name from globus client
register_dataset	Registers a set of files belonging to a session only on the server
register_session_raw_data	Registers all files corresponding to raw data files to Alyx.
rename_files_compatibility

Classes

RegistrationClient

Object that keeps the ONE instance and provides method to create sessions and register data.

register_dataset(file_list, one=None, created_by=None, repository=None, server_only=False, versions=None, default=True, dry=False, max_md5_size=None, exists=False)

Registers a set of files belonging to a session only on the server

Parameters

• file_list – (list of pathlib.Path or pathlib.Path)

• one – optional (one.api.One), current one object, will create an instance if not provided

• created_by – (string) name of user in Alyx (defaults to ‘root’)

• repository – optional: (string) name of the repository in Alyx

• server_only – optional: (bool) if True only creates on the Flatiron (defaults to False)

• versions – optional (list of strings): versions tags (defaults to ibllib version)

• default – optional (bool) whether to set as default dataset (defaults to True)

• dry – (bool) False by default

• max_md5_size – (int) maximum file in bytes to compute md5 sum (always compute if None)

defaults to None :return:

register_session_raw_data(session_path, one=None, overwrite=False, dry=False, **kwargs)

Registers all files corresponding to raw data files to Alyx. It will select files that match Alyx registration patterns.

Parameters

• session_path –

• one – one instance to work with

• overwrite – (False) if set to True, will patch the datasets. It will take very long.

If set to False (default) will skip all already registered data. :param dry: do not register files, returns the list of files to be registered :return: list of file to register :return: Alyx response: dictionary of registered files

class RegistrationClient(one=None)

Bases: object

Object that keeps the ONE instance and provides method to create sessions and register data.

create_sessions(root_data_folder, glob_pattern='**/create_me.flag', dry=False)

Create sessions looking recursively for flag files

Parameters

• root_data_folder – folder to look for create_me.flag

• dry – bool. Dry run if True

• glob_pattern – bool. Dry run if True

Returns

None

create_session(session_path)

register_sync(root_data_folder, dry=False)

Register sessions looking recursively for flag files

Parameters

• root_data_folder – folder to look for register_me.flag

• dry – bool. Dry run if True

Returns

register_session(ses_path, file_list=True, projects=None, procedures=None)

Register session in Alyx

Parameters

• ses_path – path to the session

• file_list – bool. Set to False will only create the session and skip registration

• projects –

  list of strings corresponding to project names in the database. If set to None, defaults to the subject projects. Here is how to get a list of current projects

  >>> sorted([proj['name'] for proj in one.alyx.rest('projects', 'list')])
  

• procedures – (None) list of session procedure to label the session with. They should

correspond to procedures in the database.

>>> sorted([proc['name'] for proc in one.alyx.rest('procedures', 'list')])

Returns

Status string on error

rename_files_compatibility(ses_path, version_tag)

get_local_data_repository(one)

Get local data repo name from globus client

Parameters

one –

Returns